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PubMed2005

A tiered approach to comparative genomics.

Comparative genomics has emerged as a valuable tool for locating genes, transcription factor motifs and other putative control regions. There are, however, issues that keep comparative genomics from being a straightforward process. These caveats fall into three categories: database, computational and biological. In this review paper, these caveats will be discussed and illustrated using related case studies. The National Center for Biotechnology Information and University of California Santa Cruz genome databases were used, and VISTA, LAGAN and zPicture were used as comparison tools. Based on these caveats, a tiered approach to carrying out comparative genomic studies is presented.

Algorithms↗

PubMed2002

Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis.

MOTIVATION: Microarray technology provides access to expression levels of thousands of genes at once, producing large amounts of data. These datasets are valuable only if they are annotated by sufficiently detailed experiment descriptions. However, in many databases a substantial number of these annotations is in free-text format and not readily accessible to computer-aided analysis. RESULTS: The Multi-Conditional Hybridization Intensity Processing System (M-CHIPS), a data warehousing concept, focuses on providing both structure and algorithms suitable for statistical analysis of a microarray database's entire contents including the experiment annotations. It addresses the rapid growth of the amount of hybridization data, more detailed experimental descriptions, and new kinds of experiments in the future. We have developed a storage concept, a particular instance of which is an organism-specific database. Although these databases may contain different ontologies of experiment annotations, they share the same structure and therefore can be accessed by the very same statistical algorithms. Experiment ontologies have not yet reached their final shape, and standards are reduced to minimal conventions that do not yet warrant extensive description. An ontology-independent structure enables updates of annotation hierarchies during normal database operation without altering the structure. AVAILABILITY AND SUPPLEMENTARY INFORMATION: http://www.dkfz.de/tbi/services/mchips

Algorithms↗

PubMed2002

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.

MOTIVATION: We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway databases used by those algorithms, to the prediction accuracy. RESULTS: The comparisons we performed were as follows. (1) We compared two predictions of the pathway complements of Helicobacter pylori that were computed by an early version of our pathway-prediction algorithm: prediction A used the EcoCyc E. coli pathway DB as the reference database (DB) for prediction, and prediction B used the MetaCyc pathway DB (a superset of EcoCyc) as the reference pathway DB. The MetaCyc-based prediction contained 75% more pathway predictions, but we believe a significant number of those predictions were false positives. (2) We compared two predictions of the pathway complement of H. pylori that used MetaCyc as the reference pathway DB, but that used different algorithms: the original PathoLogic algorithm, and an enhanced version of the algorithm designed to eliminate false-positive pathway predictions. The improved algorithm predicted 30\% fewer metabolic pathways than the original algorithm; all of the eliminated pathways are believed to be false-positive predictions. (3) We compared the 98 pathways predicted by the enhanced algorithm with the results of a manual analysis of the pathways of H. pylori. Results: 40 of the computationally predicted pathways were consistent with the manual analysis, 13 pathways are considered false-positive predictions, and four pathways had partially overlapping topologies. Twenty-six predicted pathways were not mentioned in the manual analysis; we believe these are correct predictions by PathoLogic that were not found by the manual analysis. Five pathways from the manual analysis were not found computationally. Agreement between the computational and manual predictions was good overall, with the computational analysis inferring many pathways that the manual analysis did not identify. Ultimately the manual analysis is also partially speculative, and therefore is not an absolute measure of correctness. The algorithm is designed to err on the side of more false positives to bring more potential pathways to the user's attention. The resulting H. pylori pathway DB is freely available at http://ecocyc.org:1555/HPY/organism-summary?object=HPY. AVAILABILITY: The Pathway Tools software is freely available to academic users, and is available to commercial users for a fee. Contact pkarp@ai.sri.com for information on obtaining the software.

Algorithms↗

PubMed2002

ENDscript: a workflow to display sequence and structure information.

UNLABELLED: ENDscript is a web server grouping popular programs such as BLAST, Multalin and DSSP. It uses as query the co-ordinates file of a protein in Protein Data Bank format and generates PostScript and png figures showing: residues conserved after a multiple alignment against homologous sequences, secondary structure elements, accessibility, hydropathy and intermolecular contacts. Thus, the user can relate quickly 1D, 2D and 3D information of a protein of known structure. AVAILABILITY: http://genopole.toulouse.inra.fr/ENDscript

Amino Acid Sequence↗

PubMed2002

The NCTU BioInfo Archive of biological data sets for bioinformatics research and experimentation.

UNLABELLED: Most of the current bioinformatics literature lacks an explicit and clear description of the data used in experiments when introducing or evaluating computational tools. Without the exact data set that was fed into computational tools in experiments, any mistaken preparation of the data for later experiments may lead to discrepancy in conclusion. The NCTU BioInfo Archive is a new web-based bioinformatic data archive. It serves as a test bed for evaluating computational tools, as a bridge to link other research communities with bioinformatics, and also as an environment full of motivations and possibilities to encourage more exploratory research in bioinformatics. AVAILABILITY: http://bioinfo.cis.nctu.edu.tw

Computational Biology↗

PubMed2003

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).

MOTIVATION: A critical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO; http://www.geneontology.org) provides a taxonomy of concepts and their attributes for annotating gene products. As GO increases in size, its ongoing construction and maintenance becomes more challenging. In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO. RESULTS: We transferred GO to Protégé-2000 in order to evaluate its suitability for GO. The graphical user interface supported browsing and editing of GO. Tools for consistency checking identified minor inconsistencies in GO and opportunities to reduce redundancy in its representation. The Protégé Axiom Language proved useful for checking ontological consistency. The PROMPT tool allowed us to track changes to GO. Using Protégé-2000, we tested our ability to make changes and extensions to GO to refine the semantics of attributes and classify more concepts. AVAILABILITY: Gene Ontology in Protégé-2000 and the associated code are located at http://smi.stanford.edu/projects/helix/gokbms/. Protégé-2000 is available from http://protege.stanford.edu.

Artificial Intelligence↗

PubMed2003

Positional candidate gene selection from livestock EST databases using Gene Ontology.

MOTIVATION: The number of expressed sequence tags (ESTs) in GenBank has now surpassed 200,000 for cattle and 100,000 for swine. The Institute of Genome Research (TIGR) has organized these sequences into approximately 60,000 non-redundant consensus sequences (identified by TIGR Gene Indices) for cattle and 40,000 for swine. Anonymous ESTs are of limited value unless they are connected to function. Functional information is difficult to manage electronically because of heterogeneity of meaning and form among databases. The Gene Ontology (GO) Consortium has produced ontologies for gene function with consistent meaning and form across species. Linking livestock EST to gene function through similarity with sequences from other annotation-rich mammals could accelerate: (1) the discovery of positional candidate genes underlying a livestock quantitative trait locus (QTL) and (2) comparative mapping between livestock and other mammals (e.g. humans, mouse and rat). We initiated this investigation to determine if incorporation of the GO into the annotation process could accelerate livestock positional candidate gene discovery. RESULTS: We have associated livestock ESTs with GO nodes through sequence similarity to the NCBI Reference Sequences (RefSeq). Positional candidate genes are identified within minutes that otherwise required days. The schema described here accommodates queries that return GO nodes from terms familiar to biologists, such as gene name, alternate/alias symbol, and OMIM phenotype. AVAILABILITY: Scripts and schema are available on request from the authors.

Animals↗

PubMed2003

Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms.

MOTIVATION: Information from fully sequenced genomes makes it possible to reconstruct strain-specific global metabolic network for structural and functional studies. These networks are often very large and complex. To properly understand and analyze the global properties of metabolic networks, methods for rationally representing and quantitatively analyzing their structure are needed. RESULTS: In this work, the metabolic networks of 80 fully sequenced organisms are in silico reconstructed from genome data and an extensively revised bioreaction database. The networks are represented as directed graphs and analyzed by using the 'breadth first searching algorithm to identify the shortest pathway (path length) between any pair of the metabolites. The average path length of the networks are then calculated and compared for all the organisms. Different from previous studies the connections through current metabolites and cofactors are deleted to make the path length analysis physiologically more meaningful. The distribution of the connection degree of these networks is shown to follow the power law, indicating that the overall structure of all the metabolic networks has the characteristics of a small world network. However, clear differences exist in the network structure of the three domains of organisms. Eukaryotes and archaea have a longer average path length than bacteria. AVAILABILITY: The reaction database in excel format and the programs in VBA (Visual Basic for Applications) are available upon request. SUPPLEMENTARY MATERIAL: Bioinformatics Online.

Archaea↗

PubMed2003

A task framework for the web interface W2H.

SUMMARY: The W3H task framework allows the execution of compound jobs utilizing the description of work and data flows in a heterogeneous bioinformatics environment using meta-data information. By means of these descriptions, the task system can schedule the necessary execution of applications available in the environment, depending on rules specified in the meta-data. By integrating this task framework into the publicly available web interface W2H, similarly based on meta-data, web access and data management are immediately available for each task description. Authors of task descriptions can base their work on the underlying classes and objects to be able to describe dependency rules between previously independent applications. The result of a compound task is given as XML data that is translated according to XSLT data into web pages or plain text to report the result of the task to the user. AVAILABILITY: Within the HUSAR environment at DKFZ http://genome.dkfz-heidelberg.de/

Database Management Systems↗

PubMed2003

QuickLIMS: facilitating the data management for DNA-microarray fabrication.

SUMMARY: QuickLIMS is a Microsoft Access-based laboratory information and management system, capable of processing all information for microarray production. The program's operational flow is protocol-based, dynamically adapting to changes of the process. It interacts with the laboratory robot and with other database systems over the network, and it represents a complete solution for the management of the entire manufacturing process. AVAILABILITY AND SUPPLEMENTARY INFORMATION: http://www.dkfz-heidelberg.de/kompl_genome/Other/QuickLims/index.html

Computer Communication Networks↗

PubMed2003

Matrix2png: a utility for visualizing matrix data.

UNLABELLED: We describe a simple software tool, 'matrix2png', for creating color images of matrix data. Originally designed with the display of microarray data sets in mind, it is a general tool that can be used to make simple visualizations of matrices for use in figures, web pages, slide presentations and the like. It can also be used to generate images 'on the fly' in web applications. Both continuous-valued and discrete-valued (categorical) data sets can be displayed. Many options are available to the user, including the colors used, the display of row and column labels, and scale bars. In this note we describe some of matrix2png's features and describe some places it has been useful in the authors' work. AVAILABILITY: A simple web interface is available, and Unix binaries are available from http://microarray.cpmc.columbia.edu/matrix2png. Source code is available on request.

Color↗

PubMed2003

Pathways database system: an integrated system for biological pathways.

MOTIVATION: During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers. RESULTS: In this paper we present an integrated system, called Pathways Database System, with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The novel features of the system include: (a) genomic information integrated with other biological data and presented from a pathway, rather than from the DNA sequence, perspective; (b) design for biologists who are possibly unfamiliar with genomics, but whose research is essential for annotating gene and genome sequences with biological functions; (c) database design, implementation and graphical tools which enable users to visualize pathways data in multiple abstraction levels, and to pose predetermined queries; and (d) an implementation that allows for web(XML)-based dissemination of query outputs (i.e. pathways data) to researchers in the community, giving them control on the use of pathways data. AVAILABILITY: Available on request from the authors.

Database Management Systems↗

PubMed2003

Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation.

MOTIVATION: Many bioinformatics data resources not only hold data in the form of sequences, but also as annotation. In the majority of cases, annotation is written as scientific natural language: this is suitable for humans, but not particularly useful for machine processing. Ontologies offer a mechanism by which knowledge can be represented in a form capable of such processing. In this paper we investigate the use of ontological annotation to measure the similarities in knowledge content or 'semantic similarity' between entries in a data resource. These allow a bioinformatician to perform a similarity measure over annotation in an analogous manner to those performed over sequences. A measure of semantic similarity for the knowledge component of bioinformatics resources should afford a biologist a new tool in their repertoire of analyses. RESULTS: We present the results from experiments that investigate the validity of using semantic similarity by comparison with sequence similarity. We show a simple extension that enables a semantic search of the knowledge held within sequence databases. AVAILABILITY: Software available from http://www.russet.org.uk.

Artificial Intelligence↗

PubMed2004

PGTdb: a database providing growth temperatures of prokaryotes.

UNLABELLED: Included in Prokaryotic Growth Temperature database (PGTdb) are a total of 1334 temperature data from 1072 prokaryotic organisms, Bacteria and Archaea: PGTdb integrates microbial growth temperature data from literature survey with their nucleotide/protein sequence and protein structure data from related databases. A direct correlation is observed between the average growth temperature of an organism and the melting temperature of proteins from the organism. Therefore, this database is useful not only for microbiologists to obtain cultivation condition, but also for biochemists and structure biologists to study the correlation between protein sequences/structures and their thermostability. In addition, the taxonomy and ribosomal RNA sequence(s) of an organism are linked through NCBI Taxonomy and the Ribosomal RNA Operon Copy Number Database umdb, respectively. PGTdb is the only integrated database on the Internet to provide the growth temperature data of the prokaryotes and the combined information of their nucleotide/protein sequences, protein structures, taxonomy and phylogeny. AVAILABILITY: http://pgtdb.csie.ncu.edu.tw

Archaea↗

PubMed2004

Tailored gene array databases: applications in mechanistic toxicology.

MOTIVATION: The development of an annotated global database suitable for a wide range of investigations is a challenging and labor-intensive task. Thus, the development of databases tailored for specific applications remains necessary. For example, in the field of toxicology, no annotated gene array databases are now available that may assist in the correlation of changes in gene activity to cellular functions and processes associated with the toxic response. RESULTS: As an example of a tailored annotated database, an attempt was made to systematize available biological information on genes present on the Affymetrix Rat Toxicology U34 GeneChip, with a focus on how the gene products relate to liver cells and their response to chemical toxins. The information collected was imbedded in a local relational database to analyze data obtained in toxicological gene array experiments with hydrazine-exposed hepatocytes. The advantages and benefits of the tailored database in the biological interpretation of the results are demonstrated.

Abstracting and Indexing↗

PubMed2004

Design and implementation of a mosquito database through an entomological ontology.

There have been constant changes in the biology and behavior of the vector and parasite involved in the transmission of malaria. There is limited interest in developing new technologies and procedures for controlling the underlying factors of this threat, which poses an enormous challenge to health systems. To understand the various vector species and their interrelations is of prime importance in understanding the transmission mechanisms of malaria in order to react efficiently. To attain this objective, we have used an ontological approach to producing a database that we consider to be our own contribution in helping to control malaria vectors if eradication has been unsuccessful in the previous control campaign.

Animals↗

PubMed2005

PatGen--a consolidated resource for searching genetic patent sequences.

UNLABELLED: Compared to the wealth of online resources covering genomic, proteomic and derived data the Bioinformatics community is rather underserved when it comes to patent information related to biological sequences. The current online resources are either incomplete or rather expensive. This paper describes, PatGen, an integrated database containing data from bioinformatic and patent resources. This effort addresses the inconsistency of publicly available genetic patent data coverage by providing access to a consolidated dataset. AVAILABILITY: PatGen can be searched at http://www.patgendb.com CONTACT: rjdrouse@patentinformatics.com.

Abstracting and Indexing↗

PubMed2005

Design and implementation of a mosquito database through an entomological ontology.

There have been constant changes in the biology and behavior of the vector and parasite involved in the transmission of malaria. There is limited interest in developing new technologies and procedures for controlling the underlying factors of this threat, which poses an enormous challenge to health systems. To understand the various vector species and their interrelations is of prime importance in understanding the transmission mechanisms of malaria in order to react efficiently. To attain this objective, we have used an ontological approach to produce a database that we consider to be our own contribution in helping to control malarial vectors if eradication has been unsuccessful in the previous control campaign.

Animals↗